Hui Ge

Fellow, Whitehead Institute 617.253.3924 phone hge@wi.mit.edu

Whitehead Fellow Hui Ge is part of a new generation of scientists working to integrate bio-informatics studies with traditional biological experiments—combining "dry lab" and "wet lab" investigations. She is using an integrated laboratory approach to study gene and protein function, work that she hopes will advance understanding of human health and disease. Ge describes this research in a 38-minute presentation. [ 220 kbps QuickTime 56 kbps]

Over the years, scientists have been generating vast amounts of biological data using a variety of laboratory techniques such as microarrays, RNA interference, and yeast two-hybrid (a process that uses yeast to discover how proteins interact with each other). As these mountains of data build, it's essential that scientists find powerful ways to cross-reference them. Ge is developing computational methods that amalgamate various data sets, work that one day will greatly accelerate the speed with which researchers identify the functions of genes and proteins. (To date, fewer than half of mammalian genes have a known function.)

So far, Ge has been using these computational methods to test biological data from the earthworm C. elegans, one of the most well-characterized animal models. She also works with these animal models in a "wet lab" in order to test and tune the accuracy of her analyses. Ge has already used this combination of tools to discover the function of certain proteins essential for early embryogenesis in C. elegans.

In her graduate work, she and her colleagues devised a way to examine how certain protein interactions are conserved across evolution. The team showed that conservation of these interactions among yeast and worms was surprisingly high.

Currently, she is focusing on building integrated approaches to help researchers understand biological processes on a system-wide level (a field of research known as systems biology), and applying these approaches to specific questions regarding embryonic development of the C. elegans.

A native of China, Ge came to the U.S. in 1999 when she was selected for a Fu Fellowship, which supports Chinese students studying at Harvard. Ge worked in Marc Vidal's lab at the Dana Farber Cancer Institute, where she earned her PhD in 2004.

Selected Publications

Zou L, Sriswasdi S, Ross B, Missiuro, PV, Liu J, and Ge H. Systematic analysis of pleiotropy in C. elegans early embryogenesis. PLoS Computational Biology  (2008) 4(2):e1000003.

Qi Y, Missiuro PE, Kapoor A, Hunter CP, Jaakkola TS, Gifford DK, Ge H. Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics (2006) 22(14):e417-23.

Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 127(6):1193-207.

Qi Y, Ge H. Modularity and dynamics of cellular networks. PLoS Computational Biology  (2006) 2(12):e174

Ge H, Player C, Zou L. Toward a global picture of development: lessons from genome-scale analysis in Caenorhabditis elegans embryonic development. Developmental Dynamics  (2006) 235(8):2009-17.

Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JJ, Hao T, Bertin N, Li N, Huang J, Fernandez A, Chuang L-S, Tao T, Tang C, Ying N, Ahringer J, Hyman AA, Sönnichsen B, Echeverri C, Roth FP, Vidal M & Piano F. Predictive models of molecular machines involved in C. elegans early embryogenesis. Nature (2005) 436(7052):861-5.

Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain P, Han JJ, Chesneau A, Hao T, Goldberg DS, Berriz GF, Li N, Martinez M, Lamesch P, Wong SL, Zhang LV, Jacotot L, Vaglio P, Reboul J, Rual J, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, van den Heuvel S, Fabio Piano F, Vandenhaute J, Sardet C, Harper JW, Gerstein M, Doucette-Stamm L, Gunsalus KC, Cusick ME, Roth FP, Hill DE, Vidal M. The C. elegans interactome project: mapping the protein network of a metazoan. Science (2004) 303(5657):540-3.

Walhout AJ, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Gunsalus KC, Schetter AJ, Morton DG, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M. Integration of interactome, phenome and transcriptome mapping data for the C. elegans germline. Current Biology (2002) 12(22):1952-8.

Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from S.cerevisiae. Nature Genetics (2001) 29(4):482-6 (Also see Nature Genetics 2003 33(1):15-7).

Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Research (2001) 11(12):2120-6.

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